{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T19:48:31Z","timestamp":1793044111308,"version":"4.5.0"},"reference-count":58,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2023,4,30]],"date-time":"2023-04-30T00:00:00Z","timestamp":1682812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agriculture and Agri-Food Canada through the Organic Science Cluster II program","award":["AIP CL-02 AGR-10383"],"award-info":[{"award-number":["AIP CL-02 AGR-10383"]}]},{"name":"Agriculture and Agri-Food Canada through the Organic Science Cluster II program","award":["GRDI-AMR PSS #1858"],"award-info":[{"award-number":["GRDI-AMR PSS #1858"]}]},{"name":"Agriculture and Agri-Food Canada through the Organic Science Cluster II program","award":["J-001262"],"award-info":[{"award-number":["J-001262"]}]},{"name":"Canadian Federal Genomic Research and Development Initiative on Antimicrobial resistance","award":["AIP CL-02 AGR-10383"],"award-info":[{"award-number":["AIP CL-02 AGR-10383"]}]},{"name":"Canadian Federal Genomic Research and Development Initiative on Antimicrobial resistance","award":["GRDI-AMR PSS #1858"],"award-info":[{"award-number":["GRDI-AMR PSS #1858"]}]},{"name":"Canadian Federal Genomic Research and Development Initiative on Antimicrobial resistance","award":["J-001262"],"award-info":[{"award-number":["J-001262"]}]},{"name":"OMFRA HQP program","award":["AIP CL-02 AGR-10383"],"award-info":[{"award-number":["AIP CL-02 AGR-10383"]}]},{"name":"OMFRA HQP program","award":["GRDI-AMR PSS #1858"],"award-info":[{"award-number":["GRDI-AMR PSS #1858"]}]},{"name":"OMFRA HQP program","award":["J-001262"],"award-info":[{"award-number":["J-001262"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>American cranberry (Vaccinium macrocarpon) and lowbush\/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p &lt; 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p &lt; 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p &lt; 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p &lt; 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p &lt; 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying\/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p &lt; 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, \u03b2-lactams, lincosamides, and trimethoprim resistance genes (p &lt; 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.<\/jats:p>","DOI":"10.3390\/microorganisms11051184","type":"journal-article","created":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T12:02:31Z","timestamp":1682942551000},"page":"1184","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces"],"prefix":"10.3390","volume":"11","author":[{"given":"Chongwu","family":"Yang","sequence":"first","affiliation":[{"name":"Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quail","family":"Das","sequence":"additional","affiliation":[{"name":"Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2062-1969","authenticated-orcid":false,"given":"Muhammad A.","family":"Rehman","sequence":"additional","affiliation":[{"name":"Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianhua","family":"Yin","sequence":"additional","affiliation":[{"name":"Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Shay","sequence":"additional","affiliation":[{"name":"Ottawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0710-6863","authenticated-orcid":false,"given":"Martin","family":"Gauthier","sequence":"additional","affiliation":[{"name":"Biological Informatics Centre of Excellence, AAFC, Saint-Hyacinthe, QC J2S 8E3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Calvin Ho-Fung","family":"Lau","sequence":"additional","affiliation":[{"name":"Ottawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Ross","sequence":"additional","affiliation":[{"name":"Summerland Research and Development Center, AAFC, Summerland, BC V0H 1Z0, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2966-345X","authenticated-orcid":false,"given":"Moussa S.","family":"Diarra","sequence":"additional","affiliation":[{"name":"Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.4081\/ijas.2013.e11","article-title":"Impacts of stocking density on the performance and welfare of broiler chickens","volume":"12","author":"Abudabos","year":"2013","journal-title":"Ital. J. Anim. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/B978-0-12-407705-8.00002-1","article-title":"A selective review of advances in coccidiosis research","volume":"83","author":"Chapman","year":"2013","journal-title":"Adv. Parasitol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.3382\/ps\/pev094","article-title":"Oxidative damage to poultry: From farm to fork","volume":"94","year":"2015","journal-title":"Poult. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1297-9716-43-74","article-title":"The successful experimental induction of necrotic enteritis in chickens by Clostridium perfringens: A critical review","volume":"43","author":"Shojadoost","year":"2012","journal-title":"Vet. Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1038\/nrg3962","article-title":"Horizontal gene transfer: Building the web of life","volume":"16","author":"Soucy","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"491","DOI":"10.4315\/0362-028X.JFP-19-269","article-title":"Prevalence and antimicrobial resistance of Salmonella from antibiotic-free broilers during organic and conventional processing","volume":"83","author":"Bailey","year":"2020","journal-title":"J. Food Prot."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"155","DOI":"10.12688\/f1000research.2-155.v1","article-title":"Prevalence of antibiotic-resistant E. coli in retail chicken: Comparing conventional, organic, kosher, and raised without antibiotics","volume":"2","author":"Millman","year":"2013","journal-title":"F1000Research."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Haque, M., Sarker, S., Islam, M., Karim, M., Kayesh, M.E.H., Shiddiky, M.J., and Anwer, M.S. (2020). Sustainable antibiotic-free broiler meat production: Current trends, challenges, and possibilities in a developing country perspective. Biology, 9.","DOI":"10.3390\/biology9110411"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Fancher, C.A., Zhang, L., Kiess, A.S., Adhikari, P.A., Dinh, T.T., and Sukumaran, A.T. (2020). Avian pathogenic Escherichia coli and Clostridium perfringens: Challenges in no antibiotics ever broiler production and potential solutions. Microorganisms, 8.","DOI":"10.20944\/preprints202009.0709.v1"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1586\/14760584.5.1.143","article-title":"Poultry coccidiosis: Recent advancements in control measures and vaccine development","volume":"5","author":"Dalloul","year":"2006","journal-title":"Expert Rev. Vaccines."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.ijpddr.2014.10.002","article-title":"Vaccination of chickens against coccidiosis ameliorates drug resistance in commercial poultry production","volume":"4","author":"Chapman","year":"2014","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1080\/03079450220148988","article-title":"Anticoccidial vaccines for broiler chickens: Pathways to success","volume":"31","author":"Williams","year":"2002","journal-title":"Avian Pathol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"101","DOI":"10.3389\/fvets.2020.00101","article-title":"Poultry coccidiosis: Design and interpretation of vaccine studies","volume":"7","author":"Soutter","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"150","DOI":"10.3389\/fvets.2020.00150","article-title":"Gut microbiota, blood metabolites, and spleen immunity in broiler chickens fed berry pomaces and phenolic-enriched extractives","volume":"7","author":"Das","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"621803","DOI":"10.3389\/fimmu.2021.621803","article-title":"Effects of vaccination against coccidiosis on gut microbiota and immunity in broiler fed bacitracin and berry pomace","volume":"12","author":"Das","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100900","DOI":"10.1016\/j.psj.2020.11.069","article-title":"Research Note: Effects of supplementing cranberry and blueberry pomaces on meat quality and antioxidative capacity in broilers","volume":"100","author":"Xu","year":"2021","journal-title":"Poult. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","article-title":"SRST2: Rapid genomic surveillance for public health and hospital microbiology labs","volume":"6","author":"Inouye","year":"2014","journal-title":"Genome Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","article-title":"MEGARes 2.0: A database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data","volume":"48","author":"Doster","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/s41592-018-0176-y","article-title":"Species-level functional profiling of metagenomes and metatranscriptomes","volume":"15","author":"Franzosa","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bib\/bbx120","article-title":"A review of methods and databases for metagenomic classification and assembly","volume":"20","author":"Breitwieser","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1080\/15538362.2017.1285264","article-title":"Characterization of pilot scale processed Canadian organic cranberry (Vaccinium macrocarpon) and blueberry (V. angustifolium) juice pressing residues and phenolic-enriched extractives. Int","volume":"17","author":"Ross","year":"2017","journal-title":"J. Fruit Sci."},{"key":"ref_23","unstructured":"Cobb-Vantress Inc. (2016). Cobb 500 Broiler Performance and Nutrition Supplement, Cobb-Vantress Inc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s40793-023-00482-0","article-title":"Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods","volume":"18","author":"Shay","year":"2023","journal-title":"Environ. Microbiome"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"pdb.prot5448","DOI":"10.1101\/pdb.prot5448","article-title":"Illumina sequencing library preparation for highly multiplexed target capture and sequencing","volume":"2010","author":"Meyer","year":"2010","journal-title":"Cold Spring Harb. Protoc."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1016\/j.psj.2019.10.036","article-title":"Effects of encapsulated cinnamaldehyde and citral on the performance and cecal microbiota of broilers vaccinated or not vaccinated against coccidiosis","volume":"99","author":"Yang","year":"2020","journal-title":"Poult. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1093\/abbs\/gmu037","article-title":"Characterization of the most abundant Lactobacillus species in chicken gastrointestinal tract and potential use as probiotics for genetic engineering","volume":"46","author":"Wang","year":"2014","journal-title":"Acta Biochim. Biophys. Sin."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13100-020-00216-w","article-title":"Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data","volume":"11","author":"Mason","year":"2020","journal-title":"Mobile DNA"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2527","DOI":"10.1128\/IAI.69.4.2527-2534.2001","article-title":"Analysis of chicken mucosal immune response to Eimeria tenella and Eimeria maxima infection by quantitative reverse transcription-PCR","volume":"69","author":"Laurent","year":"2001","journal-title":"Infect. Immun."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"13780","DOI":"10.1073\/pnas.0706625104","article-title":"Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases","volume":"104","author":"Frank","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Kathayat, D., Lokesh, D., Ranjit, S., and Rajashekara, G. (2021). Avian Pathogenic Escherichia coli (APEC): An overview of virulence and pathogenesis factors, zoonotic potential, and control strategies. Pathogens, 10.","DOI":"10.3390\/pathogens10040467"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.4315\/JFP-21-033","article-title":"Antimicrobial resistance phenotypes and genotypes of Escherichia coli isolates from broiler chickens fed encapsulated cinnamaldehyde and citral","volume":"84","author":"Yang","year":"2021","journal-title":"J. Food Prot."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"957099","DOI":"10.3389\/fsufs.2022.957099","article-title":"Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone","volume":"6","author":"Das","year":"2023","journal-title":"Front. Sustain. Food Syst."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"10706","DOI":"10.1038\/s41598-018-29082-6","article-title":"Propolis potentiates the effect of cranberry (Vaccinium macrocarpon) against the virulence of uropathogenic Escherichia coli","volume":"8","author":"Ranfaing","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/s40168-018-0590-5","article-title":"The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids","volume":"6","author":"Huang","year":"2018","journal-title":"Microbiome"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"100969","DOI":"10.1016\/j.psj.2020.12.066","article-title":"Changes in the ceca microbiota of broilers vaccinated for coccidiosis or supplemented with salinomycin","volume":"100","author":"Orso","year":"2021","journal-title":"Poult. Sci."},{"key":"ref_38","unstructured":"Guerrant, L.R. (1995). Infections of the Gastrointestinal Tract, Raven Press."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Biasato, I., Ferrocino, I., Grego, E., Dabbou, S., Gai, F., Gasco, L., Cocolin, L., Capucchio, M.T., and Schiavone, A. (2019). Gut microbiota and mucin composition in female broiler chickens fed diets including yellow mealworm (Tenebrio molitor, L.). Animals, 9.","DOI":"10.3390\/ani9050213"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1155\/1997\/642360","article-title":"Bacterial glycosulphatases and sulphomucin degradation","volume":"11","author":"Robertson","year":"1997","journal-title":"Can. J. Gastroenterol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"30169","DOI":"10.1038\/srep30169","article-title":"Cranberry-derived proanthocyanidins impair virulence and inhibit quorum sensing of Pseudomonas aeruginosa","volume":"6","author":"Maisuria","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/s13756-019-0637-9","article-title":"The anti-virulence effect of cranberry active compound proanthocyanins (PACs) on expression of genes in the third-generation cephalosporin-resistant Escherichia coli CTX-M-15 associated with urinary tract infection","volume":"8","author":"Samarasinghe","year":"2019","journal-title":"Antimicrob. Resist. Infect. Control."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Das, Q., Lepp, D., Yin, X., Ross, K., McCallum, J.L., Warriner, K., Marcone, M.F., and Diarra, M.S. (2019). Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0219163"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"7523","DOI":"10.1111\/1462-2920.15767","article-title":"Escaping the fate of Sisyphus: Assessing resistome hybridization baits for antimicrobial resistance gene capture","volume":"23","author":"Beaudry","year":"2021","journal-title":"Env. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Diarra, M.S., Block, G., Rempel, H., Oomah, B.D., Harrison, J., McCallum, J., Boulanger, S., Brouillette, \u00c9., Gattuso, M., and Malouin, F. (2013). In vitro and in vivo antibacterial activities of cranberry press cake extracts alone or in combination with \u03b2-lactams against Staphylococcus aureus. BMC Complement. Altern. Med., 13.","DOI":"10.1186\/1472-6882-13-90"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/fqs\/fyx001","article-title":"The potential of berries to serve as selective inhibitors of pathogens and promoters of beneficial microorganisms","volume":"1","author":"Lacombe","year":"2017","journal-title":"Food Qual. Saf."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"111","DOI":"10.3389\/fcell.2016.00111","article-title":"Antimicrobial activity of cationic antimicrobial peptides against gram-positives: Current progress made in understanding the mode of action and the response of bacteria","volume":"4","author":"Omardien","year":"2016","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1802333","DOI":"10.1002\/advs.201802333","article-title":"Proanthocyanidin interferes with intrinsic antibiotic resistance mechanisms of Gram-negative bacteria","volume":"6","author":"Maisuria","year":"2019","journal-title":"Adv. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"673","DOI":"10.3382\/ps\/pev022","article-title":"Effect of coccidia challenge and natural betaine supplementation on performance, nutrient utilization, and intestinal lesion scores of broiler chickens fed suboptimal level of dietary methionine","volume":"94","author":"Amerah","year":"2015","journal-title":"Poult. Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3540","DOI":"10.1016\/j.psj.2020.03.035","article-title":"Influence of coccidiosis vaccination on nutrient utilization of corn, soybean meal, and distillers dried grains with soluble in broilers","volume":"99","author":"Gautier","year":"2020","journal-title":"Poult. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"108","DOI":"10.4161\/gmic.26945","article-title":"Intestinal microbiome of poultry and its interaction with host and diet","volume":"5","author":"Pan","year":"2014","journal-title":"Gut Microbes"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"254","DOI":"10.3389\/fvets.2018.00254","article-title":"Chicken gut microbiota: Importance and detection technology","volume":"5","author":"Shang","year":"2018","journal-title":"Front. Vet. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Porcheron, G., Chanteloup, N.K., Trotereau, A., Br\u00e9e, A., and Schouler, C. (2012). Effect of fructooligosaccharide metabolism on chicken colonization by an extra-intestinal pathogenic Escherichia coli strain. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0035475"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1080\/21505594.2020.1772653","article-title":"Arachidonic acid metabolism is elevated in Mycoplasma gallisepticum and Escherichia coli co-infection and induces LTC4 in serum as the biomarker for detecting poultry respiratory disease","volume":"11","author":"Wu","year":"2020","journal-title":"Virulence"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"De Cesare, A., Sirri, F., Manfreda, G., Moniaci, P., Giardini, A., Zampiga, M., and Meluzzi, A. (2017). Effect of dietary supplementation with Lactobacillus acidophilus D2\/CSL (CECT 4529) on caecum microbiome and productive performance in broiler chickens. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0176309"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1128\/CMR.00059-12","article-title":"Antimicrobial resistance and virulence: A successful or deleterious association in the bacterial world?","volume":"26","author":"Beceiro","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s40104-022-00786-0","article-title":"Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: A review","volume":"13","author":"Mak","year":"2022","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"162006","DOI":"10.1016\/j.scitotenv.2023.162006","article-title":"Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits","volume":"784","author":"Zhang","year":"2023","journal-title":"Sci. Total Environ."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/5\/1184\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:27:28Z","timestamp":1760124448000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/5\/1184"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,30]]},"references-count":58,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2023,5]]}},"alternative-id":["microorganisms11051184"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms11051184","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,30]]}}}